I am studying bioinformatics and actually am working on a validation project. We are using the command line version of blast. We created a database of the 500 000 sequences we received (using makeblastdb) and wanted to run a blast using 500 000 sequences as query. Well. I've started that yesterday at 2 pm, and... It's still running! I was wondering, maybe we did something wrong? Is it normal for it to run so long, could I do something (appart from setting the evalue, and changing the number of threads) to speed things up? I've checked on my processor something is being done. The problem is I have no way of checking how much time is left.
Thanks in advance